WntCellCycleOdeSystem Class Reference

#include <WntCellCycleOdeSystem.hpp>

Inheritance diagram for WntCellCycleOdeSystem:

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Collaboration diagram for WntCellCycleOdeSystem:

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List of all members.

Public Member Functions
	WntCellCycleOdeSystem (double WntStimulus=0.0, const CellMutationState &rMutationState=HEALTHY)
	~WntCellCycleOdeSystem ()
void	Init ()
void	SetMutationState (const CellMutationState &rMutationState)
CellMutationState &	rGetMutationState ()
void	EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)
bool	CalculateStoppingEvent (double time, const std::vector< double > &rY)
double	CalculateRootFunction (double time, const std::vector< double > &rY)
Private Attributes
double	mk2d
double	mk3d
double	mk34d
double	mk43d
double	mk23d
double	mad
double	mJ11d
double	mJ12d
double	mJ13d
double	mJ61d
double	mJ62d
double	mJ63d
double	mKm1d
double	mkpd
double	mphi_r
double	mphi_i
double	mphi_j
double	mphi_p
double	ma2d
double	ma3d
double	ma4d
double	ma5d
double	mk16d
double	mk61d
double	mPhiE2F1
CellMutationState	mMutationState

---

Detailed Description

Represents the Mirams et al. system of ODEs, based on Swat et al. (2004) [doi:10.1093/bioinformatics/bth110] and a simple Wnt model (unpublished)

The variables are

0. r = pRb 1. e = E2F1 2. i = CycD (inactive) 3. j = CycD (active) 4. p = pRb-p 5. c = destruction complex (Active) 6. b1 = Beta-Catenin (from 1st allele) 7. b2 = Beta-Catenin (from 1st allele) 8. WntLevel

Definition at line 54 of file WntCellCycleOdeSystem.hpp.

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Constructor & Destructor Documentation

WntCellCycleOdeSystem::WntCellCycleOdeSystem	(	double	WntStimulus = 0.0,
		const CellMutationState &	rMutationState = HEALTHY
	)

Constructor.

Parameters:

	WntStimulus	is a non-dimensional Wnt value between 0 and 1. This sets up the Wnt pathway in its steady state.
	rMutationState	affects the ODE system and is given by CellMutationStates.hpp

State variables.

0. r = pRb 1. e = E2F1 (This is the S-phase indicator) 2. i = CycD (inactive) 3. j = CycD (active) 4. p = pRb-p 5. c = APC (Active) 6. b1 = Beta-Catenin (1st allele's copy) 7. b2 = Beta-Catenin (2nd allele's copy) 8. WntLevel

Definition at line 31 of file WntCellCycleOdeSystem.cpp.

References Init(), ma2d, ma3d, ma4d, ma5d, mMutationState, and AbstractOdeSystem::mpSystemInfo.

WntCellCycleOdeSystem::~WntCellCycleOdeSystem

(

void

)

Destructor.

Definition at line 98 of file WntCellCycleOdeSystem.cpp.

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Member Function Documentation

void WntCellCycleOdeSystem::Init

(

)

Initialise parameter values.

Definition at line 103 of file WntCellCycleOdeSystem.cpp.

References ma2d, ma3d, ma4d, ma5d, mad, mJ11d, mJ12d, mJ13d, mJ61d, mJ62d, mJ63d, mk16d, mk23d, mk2d, mk34d, mk3d, mk43d, mk61d, mKm1d, mkpd, mphi_i, mphi_j, mphi_p, mphi_r, and mPhiE2F1.

Referenced by WntCellCycleOdeSystem().

void WntCellCycleOdeSystem::SetMutationState

(

const CellMutationState &

rMutationState

)

Set the mutation state of the cell.

This should be called by the relevant cell cycle model before any solving of the ODE system (as it is used to evaluate the Y derivatives).

Parameters:

rMutationState

the mutation state.

Definition at line 93 of file WntCellCycleOdeSystem.cpp.

References mMutationState.

CellMutationState & WntCellCycleOdeSystem::rGetMutationState

(

)

Called by the archive function on the Wnt cell cycle model.

Returns:

mMutationState the mutation state of the cell defined by CellMutationStates.hpp

Definition at line 263 of file WntCellCycleOdeSystem.cpp.

References mMutationState.

void WntCellCycleOdeSystem::EvaluateYDerivatives	(	double	time,
		const std::vector< double > &	rY,
		std::vector< double > &	rDY
	)			[virtual]

Compute the RHS of the WntCellCycle system of ODEs.

Returns a vector representing the RHS of the ODEs at each time step, y' = [y1' ... yn']. An ODE solver will call this function repeatedly to solve for y = [y1 ... yn].

Parameters:

	time	used to evaluate the RHS.
	rY	value of the solution vector used to evaluate the RHS.
	rDY	filled in with the resulting derivatives (using Alarcons et al. (2004) system of equations).

Implements AbstractOdeSystem.

Definition at line 170 of file WntCellCycleOdeSystem.cpp.

References ma2d, ma3d, ma4d, ma5d, mad, mJ11d, mJ12d, mJ13d, mJ61d, mJ62d, mJ63d, mk16d, mk23d, mk2d, mk34d, mk3d, mk43d, mk61d, mKm1d, mkpd, mMutationState, mphi_i, mphi_j, mphi_p, mphi_r, and mPhiE2F1.

bool WntCellCycleOdeSystem::CalculateStoppingEvent	(	double	time,
		const std::vector< double > &	rY
	)			[virtual]

This also contains a calculation of dY[1], copied from EvaluateYDerivatives. Ensure they do not get out of sync!

Parameters:

	time	at which to calculate whether the stopping event has occurred
	rY	value of the solution vector used to evaluate the RHS

Returns:

whether we have reached the stopping event

Reimplemented from AbstractOdeSystem.

Definition at line 268 of file WntCellCycleOdeSystem.cpp.

References mad, mJ12d, mJ62d, mk2d, mkpd, and mPhiE2F1.

double WntCellCycleOdeSystem::CalculateRootFunction	(	double	time,
		const std::vector< double > &	rY
	)			[virtual]

When using CVODE this function is called instead of CalculateStoppingEvent. It allows the point at which rY[1] reaches 1 to be found to greater precision.

Parameters:

	time	at which to calculate whether the stopping event has occurred
	rY	value of the solution vector used to evaluate the RHS

Returns:

function value - giving CVODE an estimate of how close we are to the root.

Reimplemented from AbstractOdeSystem.

Definition at line 282 of file WntCellCycleOdeSystem.cpp.

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Member Data Documentation

double WntCellCycleOdeSystem::mk2d [private]

Parameters for the Swat et al. (2004) model Dimensional parameter k_2.

Definition at line 63 of file WntCellCycleOdeSystem.hpp.

Referenced by CalculateStoppingEvent(), EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mk3d [private]

Dimensional parameter k_3.

Definition at line 65 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mk34d [private]

Dimensional parameter k_34.

Definition at line 67 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mk43d [private]

Dimensional parameter k_2.

Definition at line 69 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mk23d [private]

Dimensional parameter k_23.

Definition at line 71 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mad [private]

Dimensional parameter a.

Definition at line 73 of file WntCellCycleOdeSystem.hpp.

Referenced by CalculateStoppingEvent(), EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mJ11d [private]

Dimensional parameter J_11.

Definition at line 75 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mJ12d [private]

Dimensional parameter J_12.

Definition at line 77 of file WntCellCycleOdeSystem.hpp.

Referenced by CalculateStoppingEvent(), EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mJ13d [private]

Dimensional parameter J_13.

Definition at line 79 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mJ61d [private]

Dimensional parameter J_13.

Definition at line 81 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mJ62d [private]

Dimensional parameter J_62.

Definition at line 83 of file WntCellCycleOdeSystem.hpp.

Referenced by CalculateStoppingEvent(), EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mJ63d [private]

Dimensional parameter J_63.

Definition at line 85 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mKm1d [private]

Dimensional parameter K_m1.

Definition at line 87 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mkpd [private]

Dimensional parameter k_p.

Definition at line 89 of file WntCellCycleOdeSystem.hpp.

Referenced by CalculateStoppingEvent(), EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mphi_r [private]

Dimensionless parameter phi_r.

Definition at line 91 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mphi_i [private]

Dimensionless parameter phi_i.

Definition at line 93 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mphi_j [private]

Dimensionless parameter phi_j.

Definition at line 95 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mphi_p [private]

Dimensionless parameter phi_p.

Definition at line 97 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::ma2d [private]

Dimensional parameter a_2.

Definition at line 99 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and WntCellCycleOdeSystem().

double WntCellCycleOdeSystem::ma3d [private]

Dimensional parameter a_3.

Definition at line 101 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and WntCellCycleOdeSystem().

double WntCellCycleOdeSystem::ma4d [private]

Dimensional parameter a_4.

Definition at line 103 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and WntCellCycleOdeSystem().

double WntCellCycleOdeSystem::ma5d [private]

Dimensional parameter a_5.

Definition at line 105 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and WntCellCycleOdeSystem().

double WntCellCycleOdeSystem::mk16d [private]

Dimensional parameter k_16.

Definition at line 107 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mk61d [private]

Dimensional parameter k_61.

Definition at line 109 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double WntCellCycleOdeSystem::mPhiE2F1 [private]

Dimensionless parameter phi_E2F1.

Definition at line 111 of file WntCellCycleOdeSystem.hpp.

Referenced by CalculateStoppingEvent(), EvaluateYDerivatives(), and Init().

CellMutationState WntCellCycleOdeSystem::mMutationState [private]

The mutation state of the cell - Wnt pathway behaviour (and hence cell cycle time) changes depending on this

Definition at line 114 of file WntCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), rGetMutationState(), SetMutationState(), and WntCellCycleOdeSystem().

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The documentation for this class was generated from the following files:

• /tmp/release_1/cancer/src/odes/WntCellCycleOdeSystem.hpp
• /tmp/release_1/cancer/src/odes/WntCellCycleOdeSystem.cpp